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| author | Efraim Flashner | 2020-03-04 04:36:21 -0600 |
|---|---|---|
| committer | Efraim Flashner | 2020-03-04 04:36:21 -0600 |
| commit | 3c3c3e830ccc4fe56f6db77e770bd533c7bdc96a (patch) | |
| tree | 4bc2383466e801b85705e278bb909c2d6656e827 /gn | |
| parent | 91e66ebbd325ba32635d1145b0402f6ab0aaeb28 (diff) | |
| download | guix-bioinformatics-3c3c3e830ccc4fe56f6db77e770bd533c7bdc96a.tar.gz | |
WIP: singlecellrshiny
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 23 |
1 files changed, 16 insertions, 7 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 6774df5..94e7010 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -14,6 +14,7 @@ #:use-module (guix build-system trivial) #:use-module (guix build-system waf) #:use-module (gnu packages) + #:use-module (gnu packages bioconductor) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages check) @@ -861,19 +862,19 @@ interest, and this app can provide values and figures for applicants to use.") (license license:gpl3)))) (define-public singlecellrshiny - (let ((commit "8061dcb477ba355de77d3e4fd3a15cf3267b56af") - (revision "1")) + (let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a") + (revision "2")) (package (name "singlecellrshiny") (version (git-version "0.0.0" revision commit)) (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/syousefi/singleCellRshiny.git") + (url "https://github.com/genenetwork/singleCellRshiny") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1pd8a9jx6ijjggsifvq66madx31h29rah5pmz4kdzfzb4fskpqz1")))) + (base32 "1rxj933s9p9r7358vnp15f7ag6c0j65r4hgr8kyirfhmp1i8xdlw")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -891,13 +892,20 @@ interest, and this app can provide values and figures for applicants to use.") (copy-recursively source targetdir) (copy-file celltypes (string-append targetdir "/CellTypes_RGC_Master_08Dec2018.csv")) (copy-file top1001 (string-append targetdir "/RobTop1001.csv")) + (substitute* (string-append targetdir "/app.R") + ; (("install.package.*") "") + ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch + (("library\\(DT\\)") "library(DT)\nlibrary(multtest)") + ) (substitute* (string-append targetdir "/global.R") (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") "shinyRappToyDataset_SiamakPlay.csv") ;; Comment out the two unreferenced files for now ;(("^rgc.*") "") - ;(("CellTypes_RGC_Master_08Dec2018.csv") celltypes) - ;(("RobTop1001.csv") top1001) + (("CellTypes_RGC_Master_08Dec2018.csv") celltypes) + (("RobTop1001.csv") top1001) + ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch + (("dim\\(sc.object.1") "dim(sc.object") ) (mkdir-p (string-append out "/bin")) (call-with-output-file app @@ -933,6 +941,7 @@ runApp(launch.browser=0, port=4208)~%\n" (propagated-inputs `(("r" ,r) ("r-dt" ,r-dt) + ("r-multtest" ,r-multtest) ("r-seurat" ,r-seurat) ("r-shiny" ,r-shiny))) (home-page "http://rn6err.opar.io/") @@ -940,7 +949,7 @@ runApp(launch.browser=0, port=4208)~%\n" (description "This is the R-Shiny programs to run some basic single cell RNA sequencing (scRNA-seq) data analysis.") - (license license:gpl3)))) + (license #f)))) (define-public seqwish (package |